clean up code

Author: Johanna

src/lib.rs

@@ -493,20 +493,21 @@ pub fn main() -> Result<(), Error> {
 
             log::info!("Reaging input genomes");
             let path = Path::new(genome_ids);
-            let file = File::open(&path)?;
+            let file = File::open(path)?;
             let reader = std::io::BufReader::new(file);
 
             // Read in genomes to
-            let ids: Vec<String> = reader.lines().filter_map(|line| line.ok()).collect();
-
+            // let ids: Vec<String> = reader.lines().filter_map(|line| line.ok()).collect();
+            let ids: Vec<String> = reader.lines().map_while(Result::ok).collect();
+            
             log::info!("Reading input metadata");
             let mut sketches: MultiSketch = MultiSketch::load(ref_db)
                 .unwrap_or_else(|_| panic!("Could not read sketch metadata from {}.skm", ref_db));
 
 
             println!("BLUB");
             // write new .skm 
-            sketches.remove_metadata(ref_db, output_file, &ids);
+            let _ = sketches.remove_metadata(output_file, &ids);
 
             // remove samples from .skd file
             log::info!("Remove genomes and writing output");

src/multisketch.rs

@@ -193,7 +193,6 @@ impl MultiSketch {
     }
     pub fn remove_metadata(
         &mut self,
-        input_prefix: &str,
         output_file_name: &str,
         genome_ids_to_remove: &[String],
     ) -> std::io::Result<()> {
@@ -207,7 +206,7 @@ impl MultiSketch {
             }
         }
         self.sketch_metadata = new_sketch_metadata;
-        self.save_metadata(output_file_name);
+        let _ = self.save_metadata(output_file_name);
         Ok(())
     }
 
@@ -255,23 +254,6 @@ impl MultiSketch {
         Ok(())
     }
 
-    // pub fn get_genome_positions(&self, genome_ids: &[String], positions: &mut Vec<usize>) {
-    //     let mut missing_ids = Vec::new();
-
-    //     for id in genome_ids {
-    //         if let Some(&position) = self.name_map.get(id) {
-    //             positions.push(position);
-    //         } else {
-    //             missing_ids.push(id.clone());
-    //         }
-    //     }
-
-    //     if !missing_ids.is_empty() {
-    //         panic!("The following genome IDs were not found: {:?}", missing_ids);
-    //     }
-
-    //     positions.sort();
-    // }
 
     // This function is called when sketches are merged, not when they are
     // first sketched (this is handled by sketch::sketch_files())

tests/common/mod.rs

@@ -37,44 +37,20 @@ impl TestSetup {
     pub fn setup() -> Self {
         let wd = assert_fs::TempDir::new().unwrap();
 
-        println!("Current working directory: {:?}", std::env::current_dir().unwrap());
-        
-        // Debug: Print FILE_IN and FILE_TEST paths
-        println!("FILE_IN constant value: {:?}", FILE_IN);
-        println!("FILE_TEST constant value: {:?}", FILE_TEST);
-        
-        let file_in_path = Path::new(FILE_IN);
-        let file_test_path = Path::new(FILE_TEST);
-        
-        println!("FILE_IN absolute path: {:?}", file_in_path.canonicalize());
-        println!("FILE_TEST absolute path: {:?}", file_test_path.canonicalize());
-        
-        // Check if the directories exist
-        println!("FILE_IN exists: {}", file_in_path.exists());
-        println!("FILE_TEST exists: {}", file_test_path.exists());
-        
-        // Attempt to create symlink for SYM_IN
-        match wd.child(SYM_IN).symlink_to_dir(file_in_path.canonicalize().unwrap_or_else(|e| {
-            panic!("Failed to canonicalize FILE_IN path: {:?}. Error: {:?}", file_in_path, e);
-        })) {
-            Ok(_) => println!("Successfully created symlink for {}", SYM_IN),
-            Err(e) => println!("Failed to create symlink for {}: {:?}", SYM_IN, e),
-        }
-        
-        // Attempt to create symlink for SYM_TEST
-        match wd.child(SYM_TEST).symlink_to_dir(file_test_path.canonicalize().unwrap_or_else(|e| {
-            panic!("Failed to canonicalize FILE_TEST path: {:?}. Error: {:?}", file_test_path, e);
-        })) {
-            Ok(_) => println!("Successfully created symlink for {}", SYM_TEST),
-            Err(e) => println!("Failed to create symlink for {}: {:?}", SYM_TEST, e),
-        }
-        
-        // Debug: Print contents of temporary directory
-        println!("Contents of temporary directory:");
-        for entry in std::fs::read_dir(&wd.path()).unwrap() {
-            let entry = entry.unwrap();
-            println!("  {:?}", entry.path());
-        }
+        wd.child(SYM_IN)
+            .symlink_to_dir(
+                Path::new(FILE_IN)
+                    .canonicalize()
+                    .expect("Could not link expected files"),
+            )
+            .unwrap();
+        wd.child(SYM_TEST)
+            .symlink_to_dir(
+                Path::new(FILE_TEST)
+                    .canonicalize()
+                    .expect("Could not link expected files"),
+            )
+            .unwrap();
 
         Self { wd }
     }